Slovakia says it will only accept Christians when it takes in Syrian refugees under a EU relocation scheme.
The country is due to receive 200 people from camps in Turkey, Italy and Greece under the EU plan to resettle 40,000 new arrivals.
Interior ministry spokesman Ivan Netik said Muslims would not be accepted because they would not feel at home.
The UN’s refugee agency (UNHCR) called on countries to take an “inclusive approach” to relocation.
But Mr Netik denied the move was discriminatory and said it was intended to ensure community cohesion.
‘Not going to like it’
The number of migrants at the EU’s borders has surged in recent months, reaching a record high of 107,500 in July. Most are Syrians, Afghans, and sub-Saharan Africans, fleeing instability or poverty
Last month, EU member states agreed to take in 32,000 asylum seekers arriving in Italy and Greece over the next two years – fewer than the 40,000 target.
The scheme was made voluntary after some nations – including Slovakia – refused to accept set quotas.
Mr Netik told the BBC: “We want to really help Europe with this migration wave but… we are only a transit country and the people don’t want to stay in Slovakia.
“We could take 800 Muslims but we don’t have any mosques in Slovakia so how can Muslims be integrated if they are not going to like it here?”
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